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Assessing allele-specific expression across multiple tissues from RNA-seq read data

Pirinen, Matti ; Lappalainen, Tuuli ; Zaitlen, Noah A. ; Dermitzakis, Emmanouil T. ; Donnelly, Peter ; McCarthy, Mark I. ; Rivas, Manuel A.

In: Bioinformatics, 2015, vol. 31, no. 15, p. 2497-2504

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    Titre
    • Assessing allele-specific expression across multiple tissues from RNA-seq read data
    Auteur
    • Pirinen, Matti. Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
    • Lappalainen, Tuuli. Department of Genetic Medicine and Development and
    • Zaitlen, Noah A.. Department of Medicine, University of California, San Francisco, CA, USA
    • Dermitzakis, Emmanouil T.. Department of Genetic Medicine and Development and
    • Donnelly, Peter. Wellcome Trust Centre for Human Genetics and
    • McCarthy, Mark I.. Wellcome Trust Centre for Human Genetics and
    • Rivas, Manuel A.. Wellcome Trust Centre for Human Genetics and
    Type de document
    • Postprint
    Identifiant OAI-PMH
    • oai:doc.rero.ch:304215
    Summary
    Motivation: RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression (GTEx) project is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data. Results: We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally. Availability and implementation: http://www.well.ox.ac.uk/~rivas/mamba/. R-sources and data examples http://www.iki.fi/mpirinen/ Contact: matti.pirinen@helsinki.fi or rivas@well.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online